rs16908114
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021801.5(MMP26):āc.780A>Gā(p.Ile260Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00332 in 1,610,454 control chromosomes in the GnomAD database, including 167 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_021801.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMP26 | NM_021801.5 | c.780A>G | p.Ile260Met | missense_variant | 8/8 | ENST00000380390.6 | |
MMP26 | NM_001384608.1 | c.570A>G | p.Ile190Met | missense_variant | 8/8 | ||
MMP26 | XM_011520219.3 | c.570A>G | p.Ile190Met | missense_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMP26 | ENST00000380390.6 | c.780A>G | p.Ile260Met | missense_variant | 8/8 | 5 | NM_021801.5 | P1 | |
MMP26 | ENST00000300762.2 | c.570A>G | p.Ile190Met | missense_variant | 8/8 | 1 | |||
MMP26 | ENST00000690848.1 | c.780A>G | p.Ile260Met | missense_variant | 7/7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0183 AC: 2782AN: 151692Hom.: 80 Cov.: 32
GnomAD3 exomes AF: 0.00480 AC: 1172AN: 244120Hom.: 45 AF XY: 0.00330 AC XY: 437AN XY: 132376
GnomAD4 exome AF: 0.00175 AC: 2550AN: 1458644Hom.: 84 Cov.: 32 AF XY: 0.00151 AC XY: 1096AN XY: 725560
GnomAD4 genome ? AF: 0.0184 AC: 2793AN: 151810Hom.: 83 Cov.: 32 AF XY: 0.0181 AC XY: 1339AN XY: 74164
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at